PDBsum entry 1ffj

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Toxin PDB id
Protein chain
60 a.a. *
Waters ×6
* Residue conservation analysis
PDB id:
Name: Toxin
Title: Nmr structure of cardiotoxin in dpc-micelle
Structure: Cytotoxin 2. Chain: a. Fragment: 1. Synonym: cardiotoxin
Source: Naja oxiana. Central asian cobra. Organism_taxid: 8657. Secretion: venom
NMR struc: 20 models
Authors: P.V.Dubovskii,D.V.Dementieva,E.V.Bocharov,Y.N.Utkin, A.S.Arseniev
Key ref:
P.V.Dubovskii et al. (2001). Membrane binding motif of the P-type cardiotoxin. J Mol Biol, 305, 137-149. PubMed id: 11114253 DOI: 10.1006/jmbi.2000.4283
25-Jul-00     Release date:   17-Jan-01    
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Protein chain
Pfam   ArchSchema ?
P01441  (CX2_NAJOX) -  Cytotoxin 2
60 a.a.
60 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     modification of morphology or physiology of other organism   2 terms 


DOI no: 10.1006/jmbi.2000.4283 J Mol Biol 305:137-149 (2001)
PubMed id: 11114253  
Membrane binding motif of the P-type cardiotoxin.
P.V.Dubovskii, D.V.Dementieva, E.V.Bocharov, Y.N.Utkin, A.S.Arseniev.
Carditoxins (CTXs) from cobra snake venoms, the basic 60-62 residue all-beta sheet polypeptides, are known to bind to and impair the function of cell membranes. To assess the membrane induced conformation and orientation of CTXs, the interaction of the P-type cardiotoxin II from Naja oxiana snake venom (CTII) with perdeuterated dodecylphosphocholine (DPC) was studied using ( 1 )H-NMR spectroscopy and diffusion measurements. Under conditions where the toxin formed a well-defined complex with DPC, the spatial structure of CTII with respect to the presence of tightly bound water molecules in loop II, was calculated using the torsion angle dynamics program DYANA. The structure was found to be similar, except for subtle changes in the tips of all three loops, to the previously described "major" form of CTII in aqueous solution illustrated by the "trans" configuration of the Val7-Pro8 peptide bond. No "minor" form with the "cis" configuration of the above bond was found in the micelle-bound state. The broadening of the CTII backbone proton signals by 5, 16-doxylstearate relaxation probes, together with modeling based on the spatial structure of CTII, indicated a periphery mode of binding of the toxin molecule to the micelle and revealed its micelle interacting domain. The latter includes a hydrophobic region of CTII within the extremities of loops I and III (residues 5-11, 46-50), the basement of loop II (residues 24-29,31-37) and the belt of polar residues encircling these loops (lysines 4,5,12,23,50, serines 11,46, histidine 31, arginine 36). It is suggested that this structural motif and the mode of binding can be realized during interaction of CTXs with lipid and biological membranes.
  Selected figure(s)  
Figure 2.
Figure 2. Differences between chemical shifts of CTII ("major" form) in aqueous solution and of CTII in the DPC micelle (DPC/CTII molar ratio 40:1 (pH 5.5), 45 °C) for a (upper panel) and NH (or d-protons for Pro-residues) (middle panel) protons, and highest chemical shift variation of side-chain protons (lower panel).
Figure 5.
Figure 5. Scatter plots of f, q, x1 angles for the 20 best DYANA structures of CTII bound to a DPC micelle. The ranges of the corresponding angles for the "major" form of CTII in aqueous solution are indicated by the bounding rectangles.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 305, 137-149) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19720036 C.K.Wang, M.L.Colgrave, D.C.Ireland, Q.Kaas, and D.J.Craik (2009).
Despite a conserved cystine knot motif, different cyclotides have different membrane binding modes.
  Biophys J, 97, 1471-1481.
PDB codes: 2kcg 2kch
19211551 C.K.Wang, S.H.Hu, J.L.Martin, T.Sjögren, J.Hajdu, L.Bohlin, P.Claeson, U.Göransson, K.J.Rosengren, J.Tang, N.H.Tan, and D.J.Craik (2009).
Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold.
  J Biol Chem, 284, 10672-10683.
PDB codes: 2k7g 3e4h
19161969 N.Mast, W.L.Liao, I.A.Pikuleva, and I.V.Turko (2009).
Combined use of mass spectrometry and heterologous expression for identification of membrane-interacting peptides in cytochrome P450 46A1 and NADPH-cytochrome P450 oxidoreductase.
  Arch Biochem Biophys, 483, 81-89.  
17603894 A.L.Lomize, I.D.Pogozheva, M.A.Lomize, and H.I.Mosberg (2007).
The role of hydrophobic interactions in positioning of peripheral proteins in membranes.
  BMC Struct Biol, 7, 44.  
16704727 N.Sapay, Y.Guermeur, and G.Deléage (2006).
Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier.
  BMC Bioinformatics, 7, 255.  
16817894 Z.O.Shenkarev, K.D.Nadezhdin, V.A.Sobol, A.G.Sobol, L.Skjeldal, and A.S.Arseniev (2006).
Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle.
  FEBS J, 273, 2658-2672.
PDB code: 1znu
15609352 T.Lazaridis (2005).
Implicit solvent simulations of peptide interactions with anionic lipid membranes.
  Proteins, 58, 518-527.  
15128311 A.V.Osipov, M.V.Astapova, V.I.Tsetlin, and Y.N.Utkin (2004).
The first representative of glycosylated three-fingered toxins. Cytotoxin from the Naja kaouthia cobra venom.
  Eur J Biochem, 271, 2018-2027.  
12660250 F.Forouhar, W.N.Huang, J.H.Liu, K.Y.Chien, W.G.Wu, and C.D.Hsiao (2003).
Structural basis of membrane-induced cardiotoxin A3 oligomerization.
  J Biol Chem, 278, 21980-21988.
PDB code: 1h0j
12709064 P.V.Dubovskii, D.M.Lesovoy, M.A.Dubinnyi, Y.N.Utkin, and A.S.Arseniev (2003).
Interaction of the P-type cardiotoxin with phospholipid membranes.
  Eur J Biochem, 270, 2038-2046.  
12080107 R.G.Efremov, P.E.Volynsky, D.E.Nolde, P.V.Dubovskii, and A.S.Arseniev (2002).
Interaction of cardiotoxins with membranes: a molecular modeling study.
  Biophys J, 83, 144-153.  
11806918 Z.O.Shenkarev, T.A.Balashova, R.G.Efremov, Z.A.Yakimenko, T.V.Ovchinnikova, J.Raap, and A.S.Arseniev (2002).
Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating.
  Biophys J, 82, 762-771.
PDB code: 1ih9
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.